Peptide-Ca complexes can promote Ca absorption. The present study aimed to determine the transport mechanism and structural characteristics of sunflower seed and peanut peptides with high Ca binding capacity with respect to developing third-generation Ca supplements and functional food ingredients. High Ca-binding fractions of 1-3 kDa sunflower seed peptide (SSP4 ) and ≥ 10 kDa peanut peptide (PP1 ) had higher amount of Ca transported than CaCl2 and two hydrolyzed proteins in Caco-2 cells. SSP4 and PP1 were separated by Ca ion metal chelate affinity chromatography, and high Ca-binding fractions were observed for SSP4 -P2 and PP1 -P2 . The amino acid sequences of SSP4 -P2 and PP1 -P2 were characterized by high-performance liquid chromatography-electrospray ionization-time of flight mass spectrometry. Seven and eight peptides were identified from SSP4 -P2 and PP1 -P2 , respectively. These peptides had molecular weights ranging from 1500 Da to 2500 Da and a large number of characteristic amino acid sequences, such as EEEQQQ, EQ-QQQ-QQ, QQ-QQQQQ, E-EEE, EE-EEQ, RR, Q-QQ-QQQ, EE-EQ-EE-Q, QQ-QQQQ, and Q-QQQQ, where 'E' is glutamic acid and 'Q' is glutamine. SSP4 and PP1 can promote Ca transport in Caco-2 cells without affecting cell permeability. The amino acid sequences of SSP4 -P2 and PP1 -P2 with high Ca-binding abilities contain characteristic sequences, such as continuous glutamic acid and glutamine, and have low molecular weights. © 2020 Society of Chemical Industry.